A new approach of estimating the modal parameters of operating piston engines is presented. The developed approach represents a combination of concepts from currently existing analyses such as the natural excitation technique (NExT), conditioned input analysis (CIA), and conditioned source analysis (CSA), and is hence termed “conditioned NExT analysis (CNA)”. NExT analysis can be employed to estimate modal parameters of structures in their naturally excited states. However, the existence of strong combustion induced periodic forcing makes the application of NExT analysis to operating engines difficult, if not impossible. CIA and CSA, built on concepts of partial and virtual coherence respectively, can effectively condition operating engine vibration data so as to remove any periodic energy associated with the process of combustion. Such conditioned operating engine vibration measurements, when combined with NExT analysis, offer a potential technique for estimating modal parameters of operating engines.The conditioned NExT methodology is initially demonstrated by computing the modal parameters of an analytically simulated frame structure subjected to a combination of random and known periodic forcing. Subsequently, the process is extended to a controlled experiment on a steel plate, designed to simulate an operating engine environment. Guided by the results of the controlled experiment, the developed technique is extended to estimate modal parameters of an operating piston engine. The results of analysis conducted on an engine under non-operating and operating conditions are compared. Results from this research indicate the potential of the developed approach to estimate operating engine modal damping ratios. Based on the findings of this research, suitable recommendations are advanced.